View source: R/plot_functions.R
upset_test_pq | R Documentation |
See upset_pq()
to plot upset.
upset_test_pq(
physeq,
fact,
var_to_test = "OTU",
min_nb_seq = 0,
na_remove = TRUE,
numeric_fonction = sum,
...
)
physeq |
(required): a |
fact |
(required): Name of the factor to cluster samples by modalities.
Need to be in |
var_to_test |
(default c("OTU")) : a vector of column present in the tax_table slot from the physeq object |
min_nb_seq |
minimum number of sequences by OTUs by samples to take into count this OTUs in this sample. For example, if min_nb_seq=2,each value of 2 or less in the OTU table will not count in the venn diagram |
na_remove |
: if TRUE (the default), NA values in fact are removed if FALSE, NA values are set to "NA" |
numeric_fonction |
(default : sum) the function for numeric vector useful only for complex plot (see examples) |
... |
Other arguments passed on to the |
A ggplot
2 plot
Adrien Taudière
upset_pq()
data(data_fungi)
if (requireNamespace("ComplexUpset")) {
upset_test_pq(data_fungi, "Height", var_to_test = c("OTU", "Class", "Guild"))
upset_test_pq(data_fungi, "Time")
}
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